It's a little after the fact, but there's a lot going on in here that I feel compelled to correct.
> anyone receiving threats online should report it to law enforcement so the person making those threats can be dealt with and so that person can't continue to terrorize other people online.
I can see how you'd think that's a good response, but calling the cops isn't a no brainer for minorities, indeed crimes against minorities are drastically underreported. There's some good information in this thread about why (freebsdgirl's reply, for instance), but there are other reasons. Dealing with law enforcement can make a problem much, much worse; google around for the experiences that victims of sexual assault have when dealing with police and the courts. Reporting crimes like this can also get you blacklisted as an "HR problem". Victims sometimes blame themselves. Reporting a crime is a huge time and money sink. Statements, testimony, attorney's fees... it all piles up (and don't forget about the wage gap!). Again I'm only scratching the surface, but there are fundamental problems with the criminal justice system that need to be resolved before "just call the cops" is an adequate recourse.
> What many people now know as safe places, however, overreach their stated goal of providing security for minorities.
But what I think you mean is that you think it's too easy to experience disproportionate consequences for violating a safe space, for example Brendan Eich was forced to resign after his donations to an anti-same-sex-marriage campaign came to light. I'm guessing you feel like that was unjust: Eich was exercising his right to free speech, and he lost his job (one could argue it was more than just a job for him).
It's not unjust. Besides the fact that everyone who pressured Eich to step down was exercising their own free speech (blog posts, board resignations, public opinion campaigns, browser boycotts), all opinions are not valid political views, and not all political views are equal or even acceptable. For example, some people believe that all first-born children should be male, and all female fetuses should be aborted until a male child is born. If any CEO donated to a campaign supporting this cause, they'd likely lose their position, as it's pretty reprehensible.
Being racist, or homophobic, or transphobic, or misogynistic, or bigoted in general, is also reprehensible. It always has been. The friction here is that these attitudes are deeply entrenched in our culture; it takes time to clean them up, and people who are slow to change their attitudes are experiencing serious consequences for things that used to be completely acceptable (yet, importantly, still reprehensible). Victims of these attitudes rightly have no patience with this effort: their whole lives they've been oppressed for who they are, and their oppressors hide behind "free speech", and "well that's just my opinion" while minorities labor under the disparate impact caused by large numbers of relatively powerful people holding these beliefs. For example, 40% of managers admit to avoiding hiring women of childbearing age because they might use maternity benefits. That creates a bias against women that goes far beyond free speech and opinion.
The state constantly has to balance everyone's rights. There are tons of examples: free speech vs. harassment; freedom of religion vs. freedom from religion; liberty vs. safety (you have to get a license to own a gun or drive a car, etc.). You're arguing that, along the free speech vs. harassment continuum, safe spaces go too far to protect minorities from harassment, balancing the right to be bigoted against the right to feel safe and not be discriminated or prejudiced against. You need to take a closer look at the current state of things, because we're far, far away from "overreach" on this issue. Minorities continue to experience wildly disproportionate levels of harassment, physical violence and injustice. Over 80% of sexual harassment claims are made by women. African-American men are far overrepresented in our prisons. The wage gap between white men and white women, men of color and women of color is real. LGBT people face the threat of violence and discrimination every day.
> If you force someoen to empathize, they aren't truly empathizing, they are remaining quiet for fear of being called a bigot and getting their reputation ruined.
If someone does not empathize with the minority experience in the US, they're either ignorant or a bigot. You can dislike the facts, but you can't disagree with them.